Taking into account that the GM doesn't roll dice.
I'd say that when the NPC takes action, the players roll the save, from here you have a choice:
1) the GM adds the NPC's skill to the difficulty number set to begin with.
2) the GM removes the amount of dice from the NODE (or adds dice if the NODE is negative) equal to the skill.
If the player succeeds that means the NPC doesn't and vice-versa.
There are more choices, these I'd use as a go to.
Personally, I treat the NPC skills like armour.